I have never used Johnny-Five before, nevertheless I was able to install it on my Edison with the command found in rwaldron/galileo-io · GitHub. I was able to compile the blink example found in the same page and it worked correctly. I believe that you are only missing mraa, I had no issues because I had already installed it.

If you are missing mraa you can download it from AlexT's Repo. Follow these instructions to do so:

That is very strange I installed the latest version of mraa and I had the same behavior as you. But I remembered that I had test it before successfully, so I uninstalled mraa and then installed a previous version, these are the steps I used:

That's weird, did you make sure to uninstall the 0.9.0 version and then install the 0.7.2 version. I had no issues after I did this. Maybe there's something odd with your board's OS, why don't you try reflashing it? You can do it with Flash Tool Lite, you can find this tool and a guide on how to use it in Intel® Edison Downloads, the latest image can also be found in the same place.

Also, a tip for flashing the Edison, somehow the USB driver that provides the virtual disk drive seems to be buggy. For me, it helped to reboot the laptop, and start the firmware upgrade with a clean OS driver. Also, I attach a serial monitor to the other serial port to monitor progress. In my case of OS X, I do:

Could you take a screenshot of the error message you are currently getting? It would help us determine the root of the issue.

The reason why the script does work when you use the XDK is because the XDK installs a version of mraa to be specifically used with the XDK project so it runs a little bit different than if you were running it directly from Linux. If you want to run the script from Linux, you will have to install a version mraa for general Linux use. I mean, they are not different versions of the same library, they are the same but they are stored in different places and can be used in different scenarios.